- $ -

• $c : countlines.php
• $contents : countlines.php
• $total : countlines.php

- a -

• a : random.cpp, random.c
• aa_xref : prfalign.cpp, prfalign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• aa_xrefseries : readmat.cpp, readmat.c, clustalw.cpp, clustalw.c
• accum : showpair.cpp, showpair.c
• alignment : prfalign.cpp, prfalign.c
• alignment_len : prfalign.cpp, prfalign.c
• allsymbols : ureadseq.c
• aln_len : prfalign.cpp, prfalign.c
• aln_path1 : prfalign.cpp, prfalign.c
• aln_path2 : prfalign.cpp, prfalign.c
• aln_weight : prfalign.cpp, prfalign.c
• amino_acid_codes : trees.cpp, trees.c, sequence.cpp, sequence.c, readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, interfac.cpp, interfac.c, calcgap.cpp, calcgap.c
• amino_acid_order : matrices.h
• aminos : ureadseq.c
• args : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• av : trees.cpp, trees.c

- b -

• blosum30mt : prfalign.cpp, prfalign.c, palign.cpp, palign.c, matrices.h
• blosum40mt : prfalign.cpp, prfalign.c, matrices.h
• blosum45mt : prfalign.cpp, prfalign.c, matrices.h, alnscore.cpp, alnscore.c
• blosum62mt2 : prfalign.cpp, prfalign.c, matrices.h
• blosum80mt : prfalign.cpp, prfalign.c, matrices.h
• boot_ntrials : trees.cpp, trees.c, param.h, interfac.cpp, interfac.c
• boot_positions : trees.cpp, trees.c
• boot_ran_seed : trees.cpp, trees.c, param.h, interfac.cpp, interfac.c
• boot_totals : trees.cpp, trees.c
• bootlabels_arg : param.h
• bootstrap_format : trees.cpp, trees.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c

- c -

• case_arg : param.h
• ch : calctree.cpp, calctree.c
• chartab : sequence.cpp, sequence.c
• check_tree : interfac.cpp, interfac.c
• cl_seq_numbers : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• clustal_name : amenu.cpp, amenu.c
• clustal_outfile : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• clustal_outname : interfac.cpp, interfac.c
• clustal_phy_tree_file : trees.cpp, trees.c
• clustal_tree_name : interfac.cpp, interfac.c
• clustalvdnamt : prfalign.cpp, prfalign.c, palign.cpp, palign.c, matrices.h
• cmd_line_file : param.h
• cmd_line_para : param.h
• cmd_line_type : interfac.cpp, interfac.c
• cmd_line_verb : param.h
• crctab : ureadseq.c
• curr_frag : showpair.cpp, showpair.c

- d -

• dayhoff_pams : dayhoff.h
• DD : prfalign.cpp, prfalign.c, palign.cpp, palign.c
• debug : sequence.cpp, sequence.c, readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, param.h, palign.cpp, palign.c, malign.cpp, malign.c, interfac.cpp, interfac.c, calctree.cpp, calctree.c, calcgap.cpp, calcgap.c, amenu.cpp, amenu.c, alnscore.cpp, alnscore.c
• def_aa_xref : readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, clustalw.cpp, clustalw.c, alnscore.cpp, alnscore.c
• def_dna_xref : readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, clustalw.cpp, clustalw.c
• diag_index : showpair.cpp, showpair.c
• displ : showpair.cpp, showpair.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c
• dist_name : amenu.cpp, amenu.c
• dist_tree_name : interfac.cpp, interfac.c
• distance_tree : prfalign.cpp, prfalign.c, malign.cpp, malign.c, clustalw.cpp, clustalw.c, calctree.cpp, calctree.c
• distances_phy_tree_file : trees.cpp, trees.c
• divergence_cutoff : param.h, malign.cpp, malign.c, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• dna_gap_extend : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• dna_gap_open : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• dna_ktup : showpair.cpp, showpair.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• dna_pw_ge_penalty : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• dna_pw_go_penalty : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• dna_signif : showpair.cpp, showpair.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• dna_wind_gap : showpair.cpp, showpair.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• dna_window : showpair.cpp, showpair.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• dna_xref : prfalign.cpp, prfalign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• dnaflag : trees.cpp, trees.c, showpair.cpp, showpair.c, sequence.cpp, sequence.c, readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, calcgap.cpp, calcgap.c, amenu.cpp, amenu.c
• dnamatnum : param.h, amenu.cpp, amenu.c
• dnamatrix_menu : interfac.cpp, interfac.c, amenu.cpp, amenu.c
• dnamtrxname : prfalign.cpp, prfalign.c, param.h, amenu.cpp, amenu.c
• dnausermtrxname : param.h

- e -

• empty : trees.cpp, trees.c, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• endgappenalties : prfalign.cpp, prfalign.c, param.h, calcgap.cpp, calcgap.c
• explicit_dnaflag : sequence.cpp, sequence.c, param.h, interfac.cpp, interfac.c

- f -

• fasta_name : amenu.cpp, amenu.c
• fasta_outfile : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• fasta_outname : interfac.cpp, interfac.c
• fd : calctree.cpp, calctree.c
• fin : sequence.cpp, sequence.c
• first_seq : trees.cpp, trees.c
• firstres : amenu.cpp, amenu.c
• formatNames : sequence.cpp, sequence.c

- g -

• g : palign.cpp, palign.c
• gap_dist : param.h, interfac.cpp, interfac.c, calcgap.cpp, calcgap.c, amenu.cpp, amenu.c
• gap_extend : prfalign.cpp, prfalign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• gap_open : prfalign.cpp, prfalign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c, alnscore.cpp, alnscore.c
• gap_penalty_mask : sequence.cpp, sequence.c, interfac.cpp, interfac.c
• gap_penalty_mask1 : prfalign.cpp, prfalign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• gap_penalty_mask2 : prfalign.cpp, prfalign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• gap_pos1 : trees.cpp, trees.c, readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, calcprf2.cpp, calcprf2.c, calcprf1.cpp, calcprf1.c
• gap_pos2 : trees.cpp, trees.c, sequence.cpp, sequence.c, readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, calcprf2.cpp, calcprf2.c, calcprf1.cpp, calcprf1.c
• gapcoef1 : prfalign.cpp, prfalign.c
• gapcoef2 : prfalign.cpp, prfalign.c
• gaps : prfalign.cpp, prfalign.c
• gb_item_type : GenBank.cpp
• gcg_outfile : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• gcg_outname : interfac.cpp, interfac.c
• gde_outfile : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• gde_outname : interfac.cpp, interfac.c
• gdist : calcgap.cpp, calcgap.c
• gFail : xmltest.cpp
• gh : palign.cpp, palign.c
• global_sort_ascending : TRestrictionEditor.cpp
• global_sort_mode : TRestrictionEditor.cpp
• gon120mt : prfalign.cpp, prfalign.c, matrices.h
• gon160mt : prfalign.cpp, prfalign.c, matrices.h
• gon250mt : prfalign.cpp, prfalign.c, palign.cpp, palign.c, matrices.h
• gon300mt : matrices.h
• gon350mt : prfalign.cpp, prfalign.c, matrices.h
• gon40mt : prfalign.cpp, prfalign.c, matrices.h
• gon80mt : prfalign.cpp, prfalign.c, matrices.h
• gPass : xmltest.cpp
• gPretty : ureadseq.h
• groups : calctree.cpp, calctree.c
• gS : prfalign.cpp, prfalign.c

- h -

• helix_end_minus : param.h, amenu.cpp, amenu.c
• helix_end_penalty : param.h, amenu.cpp, amenu.c
• helix_end_plus : param.h, amenu.cpp, amenu.c
• helix_penalty : param.h, amenu.cpp, amenu.c
• help_file_name : clustalw.cpp, clustalw.c
• HH : prfalign.cpp, prfalign.c, palign.cpp, palign.c
• hyd_residues : param.h, interfac.cpp, interfac.c, calcgap.cpp, calcgap.c, amenu.cpp, amenu.c

- i -

• idmat : prfalign.cpp, prfalign.c, palign.cpp, palign.c, matrices.h
• int_scale : palign.cpp, palign.c
• interactive : sequence.cpp, sequence.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, calctree.cpp, calctree.c

- j -

• j : random.cpp, random.c
• jmpbuf : amenu.cpp, amenu.c

- k -

• kimura : trees.cpp, trees.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• kNocountsymbols : ureadseq.c
• ktup : showpair.cpp, showpair.c, interfac.cpp, interfac.c, amenu.cpp, amenu.c

- l -

• last_print : prfalign.cpp, prfalign.c, palign.cpp, palign.c
• last_seq : trees.cpp, trees.c
• lastres : amenu.cpp, amenu.c
• left_branch : trees.cpp, trees.c
• lencoef1 : prfalign.cpp, prfalign.c
• lencoef2 : prfalign.cpp, prfalign.c
• lin1 : amenu.cpp, amenu.c
• lin2 : interfac.cpp, interfac.c, amenu.cpp, amenu.c
• lin3 : amenu.cpp, amenu.c
• loop_penalty : param.h, amenu.cpp, amenu.c
• lowercase : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• lptr : calctree.cpp, calctree.c

- m -

• mat_avscore : readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, clustalw.cpp, clustalw.c
• matnum : param.h, amenu.cpp, amenu.c
• matrix : prfalign.cpp, prfalign.c, palign.cpp, palign.c
• matrix_menu : interfac.cpp, interfac.c, amenu.cpp, amenu.c
• matseries : readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, clustalw.cpp, clustalw.c
• max_aa : showpair.cpp, showpair.c, readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, malign.cpp, malign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, calcprf2.cpp, calcprf2.c, calcprf1.cpp, calcprf1.c, calcgap.cpp, calcgap.c, alnscore.cpp, alnscore.c
• max_aln_length : trees.cpp, trees.c, showpair.cpp, showpair.c, sequence.cpp, sequence.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• max_names : trees.cpp, trees.c, sequence.cpp, sequence.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• maxscore : palign.cpp, palign.c
• maxsf : showpair.cpp, showpair.c
• mm_score : palign.cpp, palign.c
• mtrxname : prfalign.cpp, prfalign.c, param.h, amenu.cpp, amenu.c
• MyFrameType : MyFrame.h, ChildBase.h

- n -

• names : util.cpp, util.c, trees.cpp, trees.c, sequence.cpp, sequence.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, calctree.cpp, calctree.c
• nbrf_outfile : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• nbrf_outname : interfac.cpp, interfac.c
• neg_matrix : prfalign.cpp, prfalign.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• new_seq : param.h, interfac.cpp, interfac.c
• new_tree1_file : interfac.cpp, interfac.c
• new_tree2_file : interfac.cpp, interfac.c
• new_tree_file : interfac.cpp, interfac.c
• next : showpair.cpp, showpair.c
• nexus_name : amenu.cpp, amenu.c
• nexus_outfile : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• nexus_outname : interfac.cpp, interfac.c
• nexus_phy_tree_file : trees.cpp, trees.c
• nexus_tree_name : interfac.cpp, interfac.c
• nhyd_pen : calcgap.cpp, calcgap.c
• nnodes : calctree.cpp, calctree.c
• no_hyd_penalties : param.h, interfac.cpp, interfac.c, calcgap.cpp, calcgap.c, amenu.cpp, amenu.c
• no_pref_penalties : param.h, interfac.cpp, interfac.c, calcgap.cpp, calcgap.c, amenu.cpp, amenu.c
• no_var_penalties : param.h, calcgap.cpp, calcgap.c, amenu.cpp, amenu.c
• no_weights : param.h, malign.cpp, malign.c, interfac.cpp, interfac.c, calctree.cpp, calctree.c
• nonummask : ureadseq.c
• npref_pen : calcgap.cpp, calcgap.c
• nptr : calctree.cpp, calctree.c
• nseqs : trees.cpp, trees.c, showpair.cpp, showpair.c, sequence.cpp, sequence.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, malign.cpp, malign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c, alnscore.cpp, alnscore.c
• nseqs1 : prfalign.cpp, prfalign.c
• nseqs2 : prfalign.cpp, prfalign.c
• nsets : malign.cpp, malign.c, clustalw.cpp, clustalw.c, calctree.cpp, calctree.c
• ntotal : calctree.cpp, calctree.c
• nucleic_acid_order : matrices.h
• nummask : ureadseq.c
• numparams : interfac.cpp, interfac.c
• numseq : calctree.cpp, calctree.c
• nvar_pen : calcgap.cpp, calcgap.c

- o -

• olptr : calctree.cpp, calctree.c
• outfile_name : interfac.cpp, interfac.c
• outorder_arg : param.h
• output_arg : param.h
• output_clustal : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_fasta : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_gcg : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_gde : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_index : util.cpp, util.c, sequence.cpp, sequence.c, malign.cpp, malign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• output_nbrf : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_nexus : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_order : param.h, malign.cpp, malign.c, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_phylip : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_pim : trees.cpp, trees.c, param.h
• output_struct_penalties : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_tree_clustal : trees.cpp, trees.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_tree_distances : trees.cpp, trees.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_tree_nexus : trees.cpp, trees.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• output_tree_phylip : trees.cpp, trees.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• outputsecstr_arg : param.h
• outputtree_arg : param.h

- p -

• p1_tree_name : interfac.cpp, interfac.c, amenu.cpp, amenu.c
• p2_tree_name : interfac.cpp, interfac.c, amenu.cpp, amenu.c
• pal_op : calcgap.cpp, calcgap.c
• pam120mt : prfalign.cpp, prfalign.c, matrices.h
• pam160mt : prfalign.cpp, prfalign.c
• pam20mt : prfalign.cpp, prfalign.c, matrices.h
• pam350mt : prfalign.cpp, prfalign.c, palign.cpp, palign.c, matrices.h
• pam60mt : prfalign.cpp, prfalign.c, matrices.h
• param_arg : interfac.cpp, interfac.c
• params : interfac.cpp, interfac.c
• pas_op : calcgap.cpp, calcgap.c
• pas_op2 : calcgap.cpp, calcgap.c
• percent : showpair.cpp, showpair.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• phylip_name : amenu.cpp, amenu.c
• phylip_outfile : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• phylip_outname : interfac.cpp, interfac.c
• phylip_phy_tree_file : trees.cpp, trees.c
• phylip_tree_name : interfac.cpp, interfac.c
• pim_file : trees.cpp, trees.c
• pim_name : interfac.cpp, interfac.c
• pr : calcgap.cpp, calcgap.c
• prf_length1 : prfalign.cpp, prfalign.c
• prf_length2 : prfalign.cpp, prfalign.c
• primenuc : ureadseq.c
• print_ptr : prfalign.cpp, prfalign.c, palign.cpp, palign.c
• profile1 : prfalign.cpp, prfalign.c
• profile1_empty : sequence.cpp, sequence.c, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• profile1_name : interfac.cpp, interfac.c, amenu.cpp, amenu.c
• profile1_nseqs : malign.cpp, malign.c, interfac.cpp, interfac.c
• profile2 : prfalign.cpp, prfalign.c
• profile2_empty : sequence.cpp, sequence.c, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• profile2_name : interfac.cpp, interfac.c, amenu.cpp, amenu.c
• profile_no : sequence.cpp, sequence.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• profile_type : param.h
• prot_gap_extend : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• prot_gap_open : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• prot_ktup : showpair.cpp, showpair.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• prot_pw_ge_penalty : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• prot_pw_go_penalty : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• prot_signif : showpair.cpp, showpair.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• prot_wind_gap : showpair.cpp, showpair.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• prot_window : showpair.cpp, showpair.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• protonly : ureadseq.c
• ptrs : calctree.cpp, calctree.c
• pw_aa_xref : palign.cpp, palign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• pw_dna_xref : palign.cpp, palign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• pw_dnamatnum : param.h, amenu.cpp, amenu.c
• pw_dnamtrxname : param.h, palign.cpp, palign.c, amenu.cpp, amenu.c
• pw_dnausermtrxname : param.h
• pw_ge_penalty : palign.cpp, palign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• pw_go_penalty : palign.cpp, palign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• pw_matnum : param.h, amenu.cpp, amenu.c
• pw_matrix_menu : interfac.cpp, interfac.c, amenu.cpp, amenu.c
• pw_mtrxname : param.h, palign.cpp, palign.c, amenu.cpp, amenu.c
• pw_userdnamat : palign.cpp, palign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• pw_usermat : palign.cpp, palign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• pw_usermtrxname : param.h

- q -

• quick_pairalign : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c

- r -

• reduced_gap : calcgap.cpp, calcgap.c
• res_cat1 : param.h
• res_cat2 : param.h
• reset_alignments_all : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• reset_alignments_new : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• revision_level : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• right_branch : trees.cpp, trees.c
• root : calctree.cpp, calctree.c
• rooted_tree : calctree.cpp, calctree.c
• RR : prfalign.cpp, prfalign.c, palign.cpp, palign.c

- s -

• save_left_branch : trees.cpp, trees.c
• save_parameters : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• save_right_branch : trees.cpp, trees.c
• sb1 : palign.cpp, palign.c
• sb2 : palign.cpp, palign.c
• score_arg : param.h
• se1 : palign.cpp, palign.c
• se2 : palign.cpp, palign.c
• sec_struct_mask : sequence.cpp, sequence.c, interfac.cpp, interfac.c
• sec_struct_mask1 : prfalign.cpp, prfalign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• sec_struct_mask2 : prfalign.cpp, prfalign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• secstroutput_txt : amenu.cpp, amenu.c
• seq1 : palign.cpp, palign.c
• seq2 : palign.cpp, palign.c
• seq_array : util.cpp, util.c, trees.cpp, trees.c, showpair.cpp, showpair.c, sequence.cpp, sequence.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, malign.cpp, malign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, alnscore.cpp, alnscore.c
• seq_tree : calctree.cpp, calctree.c
• seq_weight : util.cpp, util.c, prfalign.cpp, prfalign.c, malign.cpp, malign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, calctree.cpp, calctree.c
• seqFormat : sequence.cpp, sequence.c
• seqlen_array : util.cpp, util.c, trees.cpp, trees.c, showpair.cpp, showpair.c, sequence.cpp, sequence.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, malign.cpp, malign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, alnscore.cpp, alnscore.c
• seqname : trees.cpp, trees.c, sequence.cpp, sequence.c, malign.cpp, malign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• seqno_arg : param.h
• seqno_range_arg : param.h
• seqRange : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• seqsymbols : ureadseq.c
• setalign : param.h
• setbatch : param.h
• setbootlabels : param.h
• setbootstrap : param.h
• setcase : param.h
• setconvert : param.h
• setdebug : param.h
• setdnamatrix : param.h
• setgapdist : param.h
• setgapext : param.h
• setgapopen : param.h
• sethelixendin : param.h
• sethelixendout : param.h
• sethelixgap : param.h
• sethelp : param.h
• sethgapres : param.h
• setinfile : param.h
• setinteractive : param.h
• setkimura : param.h
• setktuple : param.h
• setloopgap : param.h
• setmatrix : param.h
• setmaxdiv : param.h
• setnegative : param.h
• setnewtree : param.h
• setnewtree1 : param.h
• setnewtree2 : param.h
• setnohgap : param.h
• setnopgap : param.h
• setnovgap : param.h
• setnoweights : param.h
• setoptions : param.h
• setoutfile : param.h
• setoutorder : param.h
• setoutput : param.h
• setoutputtree : param.h
• setpairgap : param.h
• setprofile : param.h
• setprofile1 : param.h
• setprofile2 : param.h
• setpwdnamatrix : param.h
• setpwgapext : param.h
• setpwgapopen : param.h
• setpwmatrix : param.h
• setquicktree : param.h
• setrange : param.h
• sets : malign.cpp, malign.c, clustalw.cpp, clustalw.c, calctree.cpp, calctree.c
• setscore : param.h
• setsecstr1 : param.h
• setsecstr2 : param.h
• setsecstroutput : param.h
• setseed : param.h
• setseqno : param.h
• setseqno_range : param.h
• setsequences : param.h
• setstrandendin : param.h
• setstrandendout : param.h
• setstrandgap : param.h
• setterminalgap : param.h
• settopdiags : param.h
• settossgaps : param.h
• settransweight : param.h
• settree : param.h
• settype : param.h
• setuseendgaps : param.h
• setusetree : param.h
• setusetree1 : param.h
• setusetree2 : param.h
• setvgapres : param.h
• setwindow : param.h
• showaln : param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• signif : showpair.cpp, showpair.c, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• slopes : showpair.cpp, showpair.c
• sqlite3_temp_directory : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite3_version : win_sqlite3.h, mac_sqlite3.h, lin_sqlite3.h
• sqlite_encoding : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• sqlite_version : win_sqlite.h, mac_sqlite2.h, lin_sqlite.h
• SS : prfalign.cpp, prfalign.c, palign.cpp, palign.c
• ss_name : sequence.cpp, sequence.c, interfac.cpp, interfac.c
• ss_name1 : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• ss_name2 : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• st : TStorage.cpp
• stdsymbols : ureadseq.c
• strand_end_minus : param.h, amenu.cpp, amenu.c
• strand_end_penalty : param.h, amenu.cpp, amenu.c
• strand_end_plus : param.h, amenu.cpp, amenu.c
• strand_penalty : param.h, amenu.cpp, amenu.c
• struct_penalties : sequence.cpp, sequence.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• struct_penalties1 : prfalign.cpp, prfalign.c, param.h, interfac.cpp, interfac.c
• struct_penalties2 : prfalign.cpp, prfalign.c, param.h, interfac.cpp, interfac.c
• swgapdnamt : prfalign.cpp, prfalign.c, palign.cpp, palign.c, matrices.h
• switch_profiles : prfalign.cpp, prfalign.c

- t -

• theapp : main.cpp
• titles : util.cpp, util.c, sequence.cpp, sequence.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• TIXML_DEFAULT_ENCODING : tinyxml.h
• TIXML_MAJOR_VERSION : tinyxml.h
• TIXML_MINOR_VERSION : tinyxml.h
• TIXML_PATCH_VERSION : tinyxml.h
• tkill : trees.cpp, trees.c
• tmat : util.cpp, util.c, trees.cpp, trees.c, showpair.cpp, showpair.c, prfalign.cpp, prfalign.c, palign.cpp, palign.c, malign.cpp, malign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, calctree.cpp, calctree.c
• tossgaps : trees.cpp, trees.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• transition_weight : prfalign.cpp, prfalign.c, param.h, palign.cpp, palign.c, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• tree : interfac.cpp, interfac.c, clustalw.cpp, clustalw.c
• tree_gaps : trees.cpp, trees.c
• type_arg : param.h

- u -

• use_ambiguities : trees.cpp, trees.c, param.h, amenu.cpp, amenu.c
• use_endgaps : param.h, calcgap.cpp, calcgap.c, amenu.cpp, amenu.c
• use_ss1 : prfalign.cpp, prfalign.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• use_ss2 : prfalign.cpp, prfalign.c, param.h, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• use_tree1_file : interfac.cpp, interfac.c
• use_tree2_file : interfac.cpp, interfac.c
• use_tree_file : interfac.cpp, interfac.c
• usemenu : trees.cpp, trees.c, sequence.cpp, sequence.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, calctree.cpp, calctree.c, amenu.cpp, amenu.c
• user_series : readmat.cpp, readmat.c, prfalign.cpp, prfalign.c, clustalw.cpp, clustalw.c
• userdnamat : prfalign.cpp, prfalign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• usermat : prfalign.cpp, prfalign.c, interfac.cpp, interfac.c, clustalw.cpp, clustalw.c, amenu.cpp, amenu.c
• usermatseries : readmat.cpp, readmat.c, clustalw.cpp, clustalw.c
• usermtrxname : param.h

- v -

• vatend : showpair.cpp, showpair.c
• VDDR : CloningAssistant.h
• verbose : trees.cpp, trees.c
• vll : calcgap.cpp, calcgap.c
• vlut : calcgap.cpp, calcgap.c
• vwindow : calcgap.cpp, calcgap.c

- w -

• wind_gap : showpair.cpp, showpair.c, interfac.cpp, interfac.c, amenu.cpp, amenu.c
• window : showpair.cpp, showpair.c, interfac.cpp, interfac.c, amenu.cpp, amenu.c

- z -

• zza : showpair.cpp, showpair.c
• zzb : showpair.cpp, showpair.c
• zzc : showpair.cpp, showpair.c
• zzd : showpair.cpp, showpair.c

---